Is a female employee obligated to inform her employer about the theft of a sum of money from the store, knowing that he will have ill suspicions and that she is unable to compensate the amount?

If there was no negligence in safeguarding the money or being attentive to the shop, then you are not liable for anything. You must inform the shop owner of what happened, and entrust the matter to Allah to reveal your innocence. However, if there was negligence, then you are required to repay the money unless the shop owner pardons you.